Examining memory usage in ShortReadQ class

fastq-memory.R

library(ShortRead)

## create a single string with the number of characters defined by 'length'
## and the letter sampled from 'alphabet'
generateString <- function(length = 50, alphabet = c("A","C","G","T") ) { 
    paste0(sample(alphabet, size = length, replace = TRUE), collapse = "") 
}

## create a ShortReadQ object containing 'nreads' reads, each of which has length 'length'
createFastq <- function(nreads, length) {
    sread <- DNAStringSet( sapply(rep(length, nreads), generateString, alphabet = c("A","C","G","T") ))
    qual <- FastqQuality( sapply(rep(length, nreads), generateString, alphabet = alphabet( FastqQuality() )))
    id <- BStringSet(paste0("Read_", 1:nreads))
    fq <- ShortReadQ(sread = sread, qual = qual, id = id)
    return(fq)
}

## create 3 ShortReadQ objects - 500 reads, 50,000 reads and extract the
## first 500 reads from the larger object
fq1 <- createFastq(nreads = 500, length = 200)
fq2 <- createFastq(nreads = 50000, length = 200)
fq3 <- fq2[1:500,]

## print memory usage 
print(object.size(fq1), units = "auto") ## 229.3 Kb
print(object.size(fq2), units = "auto") ## 21.3 Mb
print(object.size(fq3), units = "auto") ## 19.6 Mb